You're probably right that the scene there was talking about when she originally searched for him as the heir to her creator, since it's showing her previous appearance before the repair and modifications. If not for that detail, I would've maybe thought the teleporter was so broken that it was now a matter of searching through both time and space. Since they were able to pull him from another world, it's not exactly weird if she'd been searching other-other worlds for where he might have teleported to. That would've really complicated matters, but in a potentially interesting sort of way. A Doctor Who style isekai, if you will.